Rv1073 Family assigned · low
H37Rv Rv1073 · MTBC0 mtbc0_001153 ·
283 aa · 1205500–1206351 (+) ·
RefSeq NP_215589.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Nicking-endonuclease-like fold (type-II nicking enzyme V.NaeI-like). RefSeq leaves it 'hypothetical protein'. |
Curated reference (UniProt)
| UniProt |
O53421
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Cullin, a subunit of E3 ubiquitin ligase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein conserved in bacteria |
| Orthologous group | COG2852 |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.658 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.21% of strains (307) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 96.3 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3r3p-assembly1_B |
1.00 | 0.72 | 8.3e-02 | 3r3p-assembly1_B Homing Endonuclease I-Bth0305I Catalytic Domain |
9g6k-assembly1_L9 |
0.66 | 0.37 | 8.8e-02 | 9g6k-assembly1_L9 LSU structure derived from the LSU sample of the mitoribosome from T. gondii. |
6z1p-assembly1_AS |
0.35 | 0.32 | 1.3e-01 | 6z1p-assembly1_AS Structure of the mitochondrial ribosome from Tetrahymena thermophila |
8bao-assembly1_B |
0.33 | 0.48 | 1.1e+00 | 8bao-assembly1_B Dysgonamonadaceae bacterium CRISPR ancillary nuclease 2 |
2inb-assembly1_A-2 |
0.20 | 0.44 | 9.5e-01 | 2inb-assembly1_A-2 Crystal structure of an XisH family protein (ZP_00107633.1) from Nostoc punctiforme PCC 73102 at 1.60 A resolution |
8b6h-assembly1_EJ |
0.18 | 0.40 | 8.4e-01 | 8b6h-assembly1_EJ Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila |
7yzm-assembly1_B |
0.16 | 0.60 | 3.7e+00 | 7yzm-assembly1_B MgADPNP-bound DCCP:DCCP-R complex |
7c2f-assembly2_D |
0.15 | 0.49 | 3.1e+00 | 7c2f-assembly2_D Crystal Structure of the Thorarchaeota ProGel/rabbit actin complex |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1072 (transmembrane protein), medium confidence from genomic context alone (score 596 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2744c 35kd_ag hyp |
hypothetical protein | 687 | 687 | coexpression:687 |
Rv2100 hyp |
hypothetical protein | 651 | 651 ctx | cooccurence:647 |
Rv3776 hyp |
hypothetical protein | 648 | 648 ctx | cooccurence:644 |
Rv1072 |
transmembrane protein | 596 | 596 ctx | neighborhood:578 |
Rv0393 hyp |
hypothetical protein | 537 | 537 ctx | cooccurence:535 |
Rv3859c gltB |
glutamate synthase large subunit | 526 | 527 | coexpression:520 |
Rv0767c |
HTH-type transcriptional regulator | 526 | 526 ctx | cooccurence:524 |
Rv0336 hyp |
hypothetical protein | 493 | 493 ctx | cooccurence:483 |
Rv0515 hyp |
hypothetical protein | 493 | 493 ctx | cooccurence:484 |
Rv3810 pirG |
cell surface protein | 492 | 492 ctx | cooccurence:489 |
Rv2345 |
transmembrane protein | 460 | 461 ctx | cooccurence:459 |
Rv3707c hyp |
hypothetical protein | 437 | 438 ctx | cooccurence:436 |
Rv0320 hyp |
hypothetical protein | 433 | 433 ctx | cooccurence:433 |
Rv3668c |
protease | 429 | 429 ctx | cooccurence:420 |
Rv0169 mce1A |
Mce family protein Mce1A | 420 | 420 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Foldseek vs AFDB-SwissProt: type II nicking enzyme V.NaeI, TM 0.55, E 1e-3
- Structural homology vs AlphaFold-Swiss-Prot (Foldseek; 542k curated SwissProt structures), project 'Still unknown gene function' phase13, 2026-06-10. Fold/family-level, not a demonstrated function.
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215589.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG2852 - Curated reference: UniProt O53421 (TrEMBL, unreviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 96.3, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
20 functional partner(s); context anchor
Rv1072 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001153|Rv1073| MGAQPFIGSEALAAGLISWHELGKYYTAIMPNVYLDKRLKPSLRQRVIAAWLWSGRKGVIAGASASALHGAKWVDDHALVELIWRNARAPNGVRTKDELLLDGEVQRLCGLTVTTVERTAFDLGRRPPLGQAITRLDALANATDFKINDVRELARKHPHTRGLRQLDKALDLVDPGAQSPKETWLRLLLINAGFPRPSTQIPLLGVYGHPKYFLDMGWEDIMLAVEYDGEQHRLSRDQFVKDVERLEYIRRAGWTHIRVLADHKGPDVVRRVRQAWDTLTSRR